Buggy code:
public class CellMLreader extends ModelReader { private Namespace mainNS ; private CellMLbioRDFblock rdfblock ; private Element rdfblockelement ; private Map < String , PhysicalModelComponent > URIandPMCmap = new HashMap < String , PhysicalModelComponent > ( ) ; private String unnamedstring = "[unnamed!]" ; private XMLOutputter xmloutputter = new XMLOutputter ( ) ; public CellMLreader ( File file ) { } public SemSimModel readFromFile ( ) { } private void collectSingularBiologicalAnnotationForSubmodel ( Document doc , FunctionalSubmodel submodel , Element comp ) { } private void processComponentRelationships ( String rel , Element comp ) { } private void getModelNameAndIDAndPubMedId ( Document doc , SemSimModel semsimmodel ) { String ab = "" ; if ( ( doc . getRootElement ( ) ) != null ) { String name = doc . getRootElement ( ) . getAttributeValue ( "name" ) ; String id = doc . getRootElement ( ) . getAttributeValue ( "id" , cmetaNS ) ; if ( ( name != null ) && ( ! ( name . equals ( "" ) ) ) ) <START_BUG> semsimmodel . setModelAnnotation ( fullname , id ) ; <END_BUG> if ( ( id != null ) && ( ! ( id . equals ( "" ) ) ) ) semsimmodel . setModelAnnotation ( sourcemodelid , id ) ; if ( ( doc . getRootElement ( ) . getChild ( "RDF" , rdfNS ) ) != null ) { if ( ( doc . getRootElement ( ) . getChild ( "RDF" , rdfNS ) . getChildren ( "Description" , rdfNS ) ) != null ) { Iterator < ? > descit = doc . getRootElement ( ) . getChild ( "RDF" , rdfNS ) . getChildren ( "Description" , rdfNS ) . iterator ( ) ; while ( descit . hasNext ( ) ) { Element nextdesc = ( ( Element ) ( descit . next ( ) ) ) ; if ( ( nextdesc . getChildren ( "reference" , bqsNS ) ) != null ) { Iterator < ? > refit = nextdesc . getChildren ( "reference" , bqsNS ) . iterator ( ) ; while ( refit . hasNext ( ) ) { Element nextref = ( ( Element ) ( refit . next ( ) ) ) ; if ( ( nextref . getChild ( "Pubmed_id" , bqsNS ) ) != null ) { String pubmedid = nextref . getChild ( "Pubmed_id" , bqsNS ) . getText ( ) ; if ( ( ! ( pubmedid . equals ( "" ) ) ) && ( pubmedid != null ) ) { ab = pubmedid ; } } } } } } } Boolean process = false ; try { doc . getRootElement ( ) . getChild ( "documentation" , docNS ) . getChild ( "article" , docNS ) . getChildren ( "sect1" , docNS ) ; process = true ; } catch ( NullPointerException e ) { System . err . println ( "Warning:<seq2seq4repair_space>in<seq2seq4repair_space>trying<seq2seq4repair_space>to<seq2seq4repair_space>parse<seq2seq4repair_space>metadata,<seq2seq4repair_space>failed<seq2seq4repair_space>to<seq2seq4repair_space>find<seq2seq4repair_space>sect1<seq2seq4repair_space>tag<seq2seq4repair_space>in<seq2seq4repair_space>model" ) ; } if ( process ) { Iterator < ? > sect1it = doc . getRootElement ( ) . getChild ( "documentation" , docNS ) . getChild ( "article" , docNS ) . getChildren ( "sect1" , docNS ) . iterator ( ) ; while ( sect1it . hasNext ( ) ) { Element nextsect1 = ( ( Element ) ( sect1it . next ( ) ) ) ; if ( nextsect1 . getAttributeValue ( "id" ) . equals ( "sec_structure" ) ) { if ( ( nextsect1 . getChildren ( "para" , docNS ) ) != null ) { Iterator < ? > it = nextsect1 . getChildren ( "para" , docNS ) . iterator ( ) ; while ( it . hasNext ( ) ) { Element nextel = ( ( Element ) ( it . next ( ) ) ) ; if ( ( nextel . getChildren ( "ulink" , docNS ) . size ( ) ) != 0 ) { Iterator < ? > ulinkit = nextel . getChildren ( "ulink" , docNS ) . iterator ( ) ; while ( ulinkit . hasNext ( ) ) { Element nextulink = ( ( Element ) ( ulinkit . next ( ) ) ) ; if ( ( nextulink . getText ( ) . toLowerCase ( ) . contains ( "pubmed<seq2seq4repair_space>id" ) ) || ( nextulink . getText ( ) . toLowerCase ( ) . contains ( "pubmedid" ) ) ) { ab = nextulink . getText ( ) ; ab = ab . substring ( ( ( ab . indexOf ( ":" ) ) + 1 ) , ab . length ( ) ) . trim ( ) ; } } } } } } } } } if ( ( ab != null ) && ( ! ( ab . equals ( "" ) ) ) ) semsimmodel . addAnnotation ( new semsim . annotation . Annotation ( CurationalMetadata . REFERENCE_PUBLICATION_PUBMED_ID_RELATION , ab ) ) ; } private void getDocumentation ( Document doc , SemSimModel semsimmodel ) { } private Element getRDFmarkupForElement ( Element el , SemSimModel semsimmodel ) { } private void stripSemSimRelatedContentFromRDFblock ( Model rdf ) { } private URI collectSingularBiologicalAnnotation ( Document doc , SemSimComponent toann , Element el ) { } private void collectCompositeAnnotation ( Document doc , SemSimComponent toann , Element el ) { } private CompositePhysicalEntity buildCompositePhysicalEntityfromRDFresource ( Resource propertyofres ) { } private PhysicalEntity getCompositeEntityComponentFromResourceAndAnnotate ( Resource res ) { } private PhysicalModelComponent getPMCfromRDFresourceAndAnnotate ( Resource res ) { } private CustomPhysicalEntity addCustomPhysicalEntityToModel ( Resource res ) { } public static Element getMathMLforOutputVariable ( String cvarname , List < ? > componentMathMLlist ) { } public static Element getElementForOutputVariableFromComponentMathML ( String cvarname , Iterator < ? > compmathmlit ) { } protected static Boolean isSolvedbyODE ( String cvarname , List < ? > componentMathMLlist ) { } protected static void whiteBoxFunctionalSubmodelEquations ( Element varmathmlel , String compname , SemSimModel semsimmodel , DataStructure cvar ) { } private String getUTFformattedString ( String str ) { } }

Fix:
semsimmodel . setModelAnnotation ( fullname , name ) ;